Protein Info for PP_4008 in Pseudomonas putida KT2440

Annotation: ATP-dependent serine protease

These analyses and tools can help you predict a protein's function, but be skeptical. For enzymes, over 10% of annotations from KEGG or SEED are probably incorrect. For other types of proteins, the error rates may be much higher. MetaCyc and Swiss-Prot have low error rates, but the best hits in these databases are often quite distant, so this protein's function may not be the same. TIGRFam has low error rates. Finally, many experimentally-characterized proteins are not in any of these databases. To find relevant papers, use PaperBLAST.

Protein Families and Features

1 50 100 150 200 250 300 350 400 450 500 550 600 650 700 756 TIGR02639: ATP-dependent Clp protease ATP-binding subunit ClpA" amino acids 3 to 739 (737 residues), 1088.3 bits, see alignment E=0 PF02861: Clp_N" amino acids 13 to 62 (50 residues), 54.9 bits, see alignment 6.3e-18 PF13191: AAA_16" amino acids 191 to 238 (48 residues), 34.6 bits, see alignment 2.2e-11 PF00004: AAA" amino acids 215 to 346 (132 residues), 45.8 bits, see alignment E=6.6e-15 amino acids 496 to 611 (116 residues), 49.9 bits, see alignment E=3.5e-16 PF17871: AAA_lid_9" amino acids 354 to 456 (103 residues), 94.1 bits, see alignment E=3.7e-30 PF07724: AAA_2" amino acids 490 to 651 (162 residues), 205.7 bits, see alignment E=4.1e-64 PF00158: Sigma54_activat" amino acids 494 to 616 (123 residues), 24.2 bits, see alignment E=1.9e-08 PF07728: AAA_5" amino acids 495 to 612 (118 residues), 53.6 bits, see alignment E=2e-17 PF10431: ClpB_D2-small" amino acids 657 to 738 (82 residues), 89.6 bits, see alignment E=8.9e-29

Best Hits

Swiss-Prot: 58% identical to CLPA_RHOBL: ClpA homolog protein from Rhodobacter blasticus

KEGG orthology group: K03694, ATP-dependent Clp protease ATP-binding subunit ClpA (inferred from 100% identity to ppf:Pput_1825)

Predicted SEED Role

"ATP-dependent Clp protease ATP-binding subunit ClpA" in subsystem Proteolysis in bacteria, ATP-dependent

Sequence Analysis Tools

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Compare to protein structures

Predict protein localization: PSORTb (Gram-negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the current SEED with FIGfam search

Find homologs in fast.genomics or the ENIGMA genome browser

See Q88FS5 at UniProt or InterPro

Protein Sequence (756 amino acids)

>PP_4008 ATP-dependent serine protease (Pseudomonas putida KT2440)
MLNRELEVTLNLAFKEARSKRHEFMTVEHLLLALLDNEAAATVLRACGANLDKLKHDLQE
FIDSTTPLIPVNDEDRETQPTLGFQRVLQRAVFHVQSSGKREVTGANVLVAIFSEQESQA
VFLLKQQSVARIDVVNYIAHGISKVPGHGAQSESEQDMQDDEGGETSSSSNPLDAYASNL
NELARAGRIDPLVGREQEVERVAQILARRRKNNPLLVGEAGVGKTAIAEGLAKRIVDGQV
PDLLAQSVVYSLDLGALLAGTKYRGDFEKRFKALLGELRKRPQAILFIDEIHTIIGAGAA
SGGVMDASNLLKPLLSSGEIRCIGSTTFQEFRGIFEKDRALARRFQKVDVSEPSVEDTVG
ILRGLKGRFESHHNIEYSDEALRAAAELASRYINDRHMPDKAIDVIDEAGAYQRLQPEAS
RVKRIDVPQVEDIVAKIARIPPKHVTSSDKELLRNLERDLKLTVFGQDQAIDSLATAIKL
SRAGLKSPDKPVGSFLFAGPTGVGKTEAARQLAKALGVELVRFDMSEYMERHTVSRLIGA
PPGYVGFDQGGLLTEAITKQPHCVLLLDEIEKAHPEVFNLLLQVMDHGTLTDNNGRKADF
RNVILIMTTNAGAETAARASIGFTHQDHASDAMEVIRKSFTPEFRNRLDTIIQFGRLSTE
TIKSIVDKFLIELQAQLEDKRVLLEVSDEARGWLAVSGYDVQMGARPMARLIQDKIKRPL
AEEILFGELAEHGGVVHVDLRDGELVFDFETTAEVA